[Biopython] Atom inheritance from Entity

[João Rodrigues]

Wouldn't it be weird for an Atom to have a get_children method? I'm
somewhat more fine with a None attribute than a useless method.

A quarta, 4/09/2019, 09:08, Spencer Bliven <spencer.bliven at gmail.com>
escreveu:

> Entity also provides methods for managing ids, transforming atoms, etc. My
> preference would be for everything to inherit from Entity and just have 0
> children. This is also consistent with Structure, which is an Entity with
> 'None' parent.
>
> -Spencer
>
>
> On 4 September 2019 at 08:02:19, João Rodrigues (
> j.p.g.l.m.rodrigues at gmail.com) wrote:
>
> Hi Spencer,
>
> Something that bugged me in the past as well. It would be nicer to have
> everyone inherit from a single point, but since Atoms don't have children,
> it would be confusing to have these methods there. My understanding is that
> Entity only exists to provide methods to handle iteration over children
> objects. It's a compromise?
>
> Thanks for the efforts in typing the module!
>
> João
>
> Spencer Bliven <spencer.bliven at gmail.com> escreveu no dia terça,
> 3/09/2019 à(s) 22:53:
>
>> I was wondering why Atom doesn't inherit from Entity. It doesn't have
>> children, but it seems like it would be more consistent to have the whole
>> Structure stack inherit from a single point. Is anyone aware of the history
>> there?
>>
>> I ask because I'm trying to add type annotations to Bio.PDB, and mypy
>> flagged a number of places where my initial 'Entity' type conflicted with
>> Atoms. We can certainly get around this by accepting either Entity or Atom,
>> but I'm not sure that was intended.
>>
>> -Spencer
>>
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>
>
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